Data sharing

Description

Shiny is an R package that makes it easy to build interactive web apps straight from R.

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Description

This plugin achieves easy creation of image figures for publications, reports, projects.

  • Easy-to-design interactive figure layout.

  • Visually assign image content to panels.

  • High-quality image scaling and rotation.

  • Easy and consistent panel labels and scale bars.

  • Each panel has it's original datasource's properties and tracks achieved image processing.

  • Save and re-open editable figures.

  • Export as standard image formats with textual description of each panel history.

Compared to Make montage, the plugin adds more flexibility to montage creation: Easy-to-design interactive figure layout. Visually assign image content to panels. High-quality image scaling and rotation. Easy and consistent panel labels and scale bars. Each panel has it's original data source's properties and tracks achieved image processing. Save and re-open editable figures. Export as standard image formats with textual description of each panel history. 

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Description

MyTardis is free and open-source data management software. It facilitates annotation, sharing and archiving of data and metadata collected from different modalities. It focuses on integration with scientific instruments, instrument facilities and research storage and computing infrastructure; to address the challenges of data storage, data access, collaboration and data publication. It is currently being used to capture data from areas such as optical microscopy, electron microscopy, medical imaging, protein crystallography, neutron and X-ray scattering, flow cytometry, genomics and proteomics.

Key features:

  • Easy instrument integration.
  • Discipline specific: MX, Imaging, Microscopy, Genomics ...
  • Wide range of data formats & supported instruments.
  • Secure cloud data storage & access.
  • Simple data sharing.
  • Researcher controlled data publishing.
  • APIs for programmatic access to data and metadata.
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Description

The Huygens Remote Manager is an open-source, efficient, multi-user web-based interface to the Huygens software by Scientific Volume Imaging for parallel batch deconvolutions.

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Description

Cytomine is a rich internet application using modern web and distributed technologies (Grails, HTML/CSS/Javascript, Docker), databases (spatial SQL and NoSQL), and machine learning (tree-based approaches with random subwindows) to foster active and distributed collaboration and ease large-scale image exploitation.

It provides remote and collaborative principles, rely on data models that allow to easily organize and semantically annotate imaging datasets in a standardized way (using user-defined ontologies associated to regions of interest), efficiently support high-resolution multi-gigapixel images (incl. major digital scanner image formats), and provide mechanisms to readily proofread and share image quantifications produced by any image recognition algorithms.

By emphasizing collaborative principles, the aim of Cytomine is to accelerate scientific progress and to significantly promote image data accessibility and reusability. Cytomine allows to break common practices in this domain where imaging datasets, quantification results, and associated knowledge are still often stored and analyzed within the restricted circle of a specific laboratory.

This software is e.g. being used by life scientists in to help them better evaluate drug treatments or understand biological processes directly from whole-slide tissue images (digital histology), by pathologists to share and ease their diagnosis, and by teachers and students for pathology training purposes. It is also used in various microscopy applications.

Cytomine can be used as a stand-alone application (e.g. on a laptop) or on larger servers for collaborative works.

Cytomine implements object classification, image segmentation, content-based image retrieval, object counting, and interest point detection algorithms using machine learning.

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